strand_occurrences: Count occurrences per base substitution type and strand

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Count occurrences per base substitution type and strand

Description

For each base substitution type and strand the total number of mutations and the relative contribution within a group is returned.

Usage

strand_occurrences(mut_mat_s, by = NA)

Arguments

mut_mat_s	192 feature mutation count matrix, result from 'mut_matrix_stranded()'
by	Character vector with grouping info, optional

Value

A data.frame with the total number of mutations and relative contribution within group per base substitution type and strand

See Also

mut_matrix_stranded, plot_strand, plot_strand_bias

Examples

## See the 'mut_matrix_stranded()' example for how we obtained the
## following mutation matrix.
mut_mat_s <- readRDS(system.file("states/mut_mat_s_data.rds",
  package = "MutationalPatterns"
))

## Load a reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

tissue <- c(
  "colon", "colon", "colon",
  "intestine", "intestine", "intestine",
  "liver", "liver", "liver"
)

strand_counts <- strand_occurrences(mut_mat_s, by = tissue)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.